5OKZ Rna Binding Protein date Jul 26, 2017
title Crystal Strucrure Of The Mpp6 Exosome Complex
authors S.Falk, J.Ebert, E.Conti
compound source
Molecule: Exosome Complex Component Csl4
Chain: m, I, S, c
Synonym: Cep1 Synthetic Lethal Protein 4
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Csl4, Ski4, Ynl232w, N1154
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Rrp45
Chain: A, K, U, e
Synonym: Ribosomal Rna-Processing Protein 45
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Rrp45, Ydr280w, D9954.1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Ski6
Chain: B, L, V, f
Synonym: Extracellular Mutant Protein 20,Ribosomal Rna-Proc Protein 41,Superkiller Protein 6;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Ski6, Ecm20, Rrp41, Ygr195w, G7587
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Rrp43
Chain: C, M, W, g
Synonym: Ribosomal Rna-Processing Protein 43
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Rrp43, Ycr035c, Ycr35c, Ycr522
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Rrp46
Chain: D, N, X, h
Synonym: Ribosomal Rna-Processing Protein 46
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Rrp46, Ygr095c
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Rrp42
Chain: E, O, Y, I
Synonym: Ribosomal Rna-Processing Protein 42
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Rrp42, Ydl111c
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Mtr3
Chain: F, P, Z, j
Synonym: Mrna Transport Regulator 3
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Mtr3, Ygr158c, G6676
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Rrp40
Chain: G, Q, a, k
Synonym: Ribosomal Rna-Processing Protein 40
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Rrp40, Yol142w
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Exosome Complex Component Rrp4
Chain: H, R, b, l
Synonym: Ribosomal Rna-Processing Protein 4
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Rrp4, Yhr069c
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: M-Phase Phosphoprotein 6 Homolog
Chain: J, T, d, n
Synonym: Exosome-Associated Rna-Binding Protein Mpp6
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Gene: Mpp6, Ynr024w, N3230
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
161.779 237.430 201.895 90.00 110.37 90.00
method X-Ray Diffractionresolution 3.20 Å
Gene
Ontology
ChainFunctionProcessComponent
B, V, L, f

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • H, b, l, R


    K, e, U, A

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • N, D, h, X

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • S, c, I, m

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • T, d, J, n


    Y, E, i, O

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • a, k, G, Q

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • g, W, M, C

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • j, Z, F, P

  • nuclear exosome (RNase compl...
  • cytoplasmic exosome (RNase c...
  • Primary referenceMpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase., Falk S, Bonneau F, Ebert J, Kogel A, Conti E, Cell Rep. 2017 Sep 5;20(10):2279-2286. doi: 10.1016/j.celrep.2017.08.033. PMID:28877463
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2946 Kb) [Save to disk]
  • Biological Unit Coordinates (5okz.pdb1.gz) 741 Kb
  • Biological Unit Coordinates (5okz.pdb2.gz) 735 Kb
  • Biological Unit Coordinates (5okz.pdb3.gz) 735 Kb
  • Biological Unit Coordinates (5okz.pdb4.gz) 750 Kb
  • CSU: Contacts of Structural Units for 5OKZ
  • Structure Factors (3957 Kb)
  • Retrieve 5OKZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OKZ from S2C, [Save to disk]
  • View 5OKZ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5OKZ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5okz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5okz_c] [5okz_I] [5okz_B] [5okz_M] [5okz_A] [5okz_k] [5okz_N] [5okz_g] [5okz_P] [5okz_e] [5okz_H] [5okz_h] [5okz_V] [5okz_m] [5okz_G] [5okz_b] [5okz_j] [5okz_R] [5okz_C] [5okz_l] [5okz_W] [5okz_O] [5okz_d] [5okz_f] [5okz_X] [5okz_T] [5okz_F] [5okz_L] [5okz_K] [5okz_n] [5okz_S] [5okz_D] [5okz_Q] [5okz_i] [5okz_Z] [5okz_U] [5okz_J] [5okz_E] [5okz_a] [5okz_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OKZ
  • Community annotation for 5OKZ at PDBWiki (http://pdbwiki.org)

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